deseq_coef: You could just call DESeq() in your code... or you could call...

In kmuench/DESeqAid: DESeqAid: Kristin's favorite functions for her DESeq-based differential expression pipelines

Description

Returns DESeq results object.

Usage

deseq_coef(dds, myAlpha, coefficient, nickname, currDate, expName,
  amySexGenes)

Arguments

dds	DESeq object
myAlpha	number - threshold for calling genes significant
coefficient	coefficient for which you want DE gene list. To see all available, enter matrix(resultsNames(dds_sva)) in command line
nickname	Character string - what do you want these results to be called
currDate	Character string - code representing date on which you did this analysis
expName	Character string - code representing this whole set of analyses
genesOfInterest	Dataframe column listing genes you might want to count in plot, e.g. sex marker genes

Details

This one takes in a coefficient from matrix(resultsNames(dds_sva)). There is also deseq_contrasts if you want to compare specific known groups.

Examples

results_SexEffect_mainEffect <- deseq_contrasts(dds_sva, 0.05, 'SexF.TimepointSecond.Trimester', 'results_SexEffect_mainEffect', '20180814', 'exploreNewData', amySexGenes[,2])

kmuench/DESeqAid documentation built on Oct. 14, 2020, 4:45 a.m.